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Zinc in PDB 4gwd: Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex

Enzymatic activity of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex

All present enzymatic activity of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex, PDB code: 4gwd was solved by E.L.D'antonio, Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.53
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.082, 91.082, 69.903, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 21.5

Other elements in 4gwd:

The structure of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex (pdb code 4gwd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex, PDB code: 4gwd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gwd

Go back to Zinc Binding Sites List in 4gwd
Zinc binding site 1 out of 2 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.0
occ:1.00
OE2 A:GLU277 2.1 19.9 1.0
O A:HOH501 2.2 15.3 1.0
ND1 A:HIS141 2.2 17.6 1.0
O3 A:ABH404 2.3 17.6 1.0
O2 A:ABH404 2.5 15.8 1.0
CD A:GLU277 2.7 17.5 1.0
B A:ABH404 2.8 15.3 1.0
CE1 A:HIS141 3.0 16.1 1.0
CG A:HIS141 3.2 14.7 1.0
OE1 A:GLU277 3.3 17.0 1.0
CE A:ABH404 3.6 14.3 1.0
CB A:HIS141 3.6 14.8 1.0
CG A:GLU277 3.7 16.5 1.0
O1 A:ABH404 4.0 17.2 1.0
NE2 A:HIS141 4.1 15.7 1.0
O A:HOH502 4.2 15.0 1.0
CD2 A:HIS141 4.2 14.1 1.0
OG1 A:THR246 4.2 15.1 1.0
N A:HIS101 4.4 20.6 1.0
CD A:ABH404 4.4 14.8 1.0
CB A:HIS101 4.5 16.3 1.0
MN A:MN402 4.5 16.1 1.0
OD2 A:ASP232 4.5 15.4 1.0
O A:HIS141 4.6 13.2 1.0
CG A:GLN19 4.7 17.5 1.0
O A:HOH560 4.7 28.7 1.0
CB A:GLU277 4.8 16.7 1.0
CA A:HIS141 4.8 14.1 1.0
C A:HIS141 4.9 14.3 1.0
OD2 A:ASP234 4.9 17.5 1.0
CB A:ASP100 4.9 19.4 1.0

Zinc binding site 2 out of 2 in 4gwd

Go back to Zinc Binding Sites List in 4gwd
Zinc binding site 2 out of 2 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:26.7
occ:1.00
O B:HOH501 2.2 18.3 1.0
OE2 B:GLU277 2.4 26.8 1.0
O3 B:ABH404 2.4 24.3 1.0
ND1 B:HIS141 2.4 18.9 1.0
O2 B:ABH404 2.5 22.6 1.0
CD B:GLU277 2.8 24.1 1.0
B B:ABH404 2.9 24.7 1.0
CE1 B:HIS141 3.2 18.1 1.0
OE1 B:GLU277 3.2 26.8 1.0
CG B:HIS141 3.3 20.2 1.0
CG B:GLU277 3.6 19.4 1.0
CE B:ABH404 3.6 23.8 1.0
CB B:HIS141 3.7 21.3 1.0
O1 B:ABH404 4.1 24.0 1.0
OG1 B:THR246 4.2 19.8 1.0
NE2 B:HIS141 4.2 17.0 1.0
O B:HOH503 4.2 16.7 1.0
OD2 B:ASP232 4.3 17.1 1.0
CD2 B:HIS141 4.3 18.0 1.0
MN B:MN402 4.5 19.3 1.0
CD B:ABH404 4.5 25.1 1.0
N B:HIS101 4.5 18.6 1.0
O B:HOH502 4.6 25.4 1.0
O B:HIS141 4.6 18.7 1.0
CB B:HIS101 4.7 19.4 1.0
CB B:GLU277 4.7 17.1 1.0
CB B:ASP100 4.7 19.6 1.0
OD2 B:ASP234 4.7 18.5 1.0
MN B:MN401 4.8 18.5 1.0
CG B:GLN19 4.9 21.7 1.0
C B:HIS141 4.9 19.6 1.0
CA B:HIS141 4.9 20.1 1.0

Reference:

E.L.D'antonio, Y.Hai, D.W.Christianson. Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry V. 51 8399 2012.
ISSN: ISSN 0006-2960
PubMed: 23061982
DOI: 10.1021/BI301145N
Page generated: Wed Dec 16 05:21:02 2020

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